After taking a postgraduate course in Prague, he returned to Berlin in 1862, where he practised until 1864, when he took service as surgeon in the war against Denmark.

In the fall of the same year he became assistant at the pathological institute of Berlin University under Rudolf Virchow, remaining there until 1868.

During this time he published several articles relating to physiological chemistry and histology, but finally turned his especial attention to pathological anatomy.

In it he proved that the emigration of the white blood-corpuscles is the origin of pus, a statement which produced a great revolution in pathology.

Cohnheim was the first to use the now universal method of freezing fresh pathological objects for examination; he also first demonstrated nerve-termination in "Cohnheim's areas" (polygonal areas indicating the cut ends of muscle-columns, seen in the cross-sections of striated muscle-fiber); he was the pioneer in the theory of inflammation, which is now universally accepted; and his researches in the field of pathological circulation and the causes of embolism marked a new departure in the methods of medical treatment.